alignment_path = "alignment.phylip"

POINTS_PATH = "points.txt"
CRAN_PATH = "r_plot.cran"

#                                                                                                              
# Build the PHYML command (pc)                                                                                 
#                                                                                                              
pc = {}
pc["--input"] = alignment_path
pc["--datatype"] = "nt"
pc["--model"] = "HKY"
pc["--support"] = "0"
pc["-f"] = [0.1100, 0.3939, 0.3929, 0.1032]
pc["-t"] = 0.469
pc["--nclasses"] = 1
pc["--blclasses"] = 1
pc["-v"] = 0.0
pc["-o"] = "n"

xmin = 0.44
xmax = 0.54
ymin = 0.170
ymax = 0.175
step = 0.001

# initialize xvar and yvar.  They will be perturbed as the analysis proceeds.                                                                            
xvar = pc["-t"]
yvar = ymin

newicktree = "((((((t14:" + yvar.__str__() + ",t13:0.1567233152):0.1317908563,(t16:0.1799901195,t15:0.1664814686):0.1229767713):0.1576037348,((t12:0.1710940999,t11:0.1783838091):0.1277599490,(t10:0.1760942864,t9:0.1938890361):0.1182664553):0.1457022308):0.1149340546,(((t8:0.1597611140,t7:0.1652645170):0.1692910191,(t6:0.1651239940,t5:0.1672591867):0.1566579249):0.0982534744,((t4:0.1442042463,t3:0.1923333981):0.1347365909,(t2:0.166514376\5,t1:0.1652216601):0.1589893867):0.1481001485):0.1138266048):0.3061388680,(t20:0.1730943632,t19:0.1427592301):0.1477775312):0.1566239065,t18:0.1628747457,t17:0.1206262480);"